What is happening here? Boolean modifier works *almost*
You can do this with the new (blender 2.76+) intersect (boolean) feature.


Steps to recreate:


Go to edit mode (Tab).
Select all (A).
Extrude inwards (E).
Go to Face select mode (CtrlTab).
Extrude individual (Tools panel-->Add-->Extrude Individual) outwards.
Select entire inner mesh island (CtrlL).
Open dynamic spacebar menu (Space).
Type in "Intersect (Boolean)" and confirm.